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1 """
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2 From a list of platewells retrieves the enrollments code of the connected individual
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3 """
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4 import argparse
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5 import csv
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6 import sys
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7
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8 from bl.vl.kb import KnowledgeBase as KB
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9 import bl.vl.utils.ome_utils as vlu
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10 from bl.vl.utils import LOG_LEVELS, get_logger
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11
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12 def make_parser():
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13 parser = argparse.ArgumentParser(description='From platewells 2 enrollments code')
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14 parser.add_argument('--logfile', type=str, help='log file (default=stderr)')
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15 parser.add_argument('--loglevel', type=str, choices = LOG_LEVELS,
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16 help='logging level', default='INFO')
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17 parser.add_argument('-H', '--host', type=str, help='omero hostname')
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18 parser.add_argument('-U', '--user', type=str, help='omero user')
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19 parser.add_argument('-P', '--passwd', type=str, help='omero password')
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20 parser.add_argument('-S', '--study', type=str, required=True,
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21 help='a study used to retrieve individuals')
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22 parser.add_argument('--ifile', type=str, required=True,
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23 help='list of platewells used to fetch data')
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24 parser.add_argument('--ofile', type=str, help='output file path',
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25 required=True)
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26 return parser
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27
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28
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29 def main(argv):
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30 parser = make_parser()
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31 args = parser.parse_args(argv)
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32
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33 logger = get_logger('pws2enrolls', level=args.loglevel,
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34 filename=args.logfile)
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35 try:
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36 host = args.host or vlu.ome_host()
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37 user = args.user or vlu.ome_user()
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38 passwd = args.passwd or vlu.ome_passwd()
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39 except ValueError, ve:
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40 logger.critical(ve)
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41 sys.exit(ve)
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42
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43 kb = KB(driver='omero')(host, user, passwd)
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44 study = kb.get_study(args.study)
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45 enrolled_map = {e.individual.id:e for e in kb.get_enrolled(study)}
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46 logger.info('Loaded {} enrolled individuals for study {}'.format(len(enrolled_map), study.label))
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47 plates = kb.get_objects(kb.TiterPlate)
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48 logger.info('Loaded {} plates'.format(len(plates)))
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49 pws_map = {':'.join([w.container.barcode, w.label]):w for w in kb.get_objects(kb.PlateWell)
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50 if w.container.barcode}
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51 logger.info('Loaded {} platewells'.format(len(pws_map)))
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52 #records = []
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53 of=open(args.ofile, 'w')
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54 writer=csv.DictWriter(of, ['platewell', 'status', 'enrollment'],
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55 delimiter='\t', quotechar='"', restval='None')
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56 writer.writeheader()
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57 with open(args.ifile, 'r') as f:
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58 reader=csv.DictReader(f, delimiter='\t')
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59 logger.info('Searching individuals connected to the platewells')
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60 for r in reader:
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61 ind=kb.dt.get_connected(pws_map[r['platewell']], kb.Individual,
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62 kb.dt.DIRECTION_INCOMING)
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63 try:
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64 record = {'platewell': r['platewell'],
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65 'status': pws_map[r['platewell']].status.enum_label(),
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66 'enrollment': ':'.join([study.label,enrolled_map[ind[0].id].studyCode])}
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67 except KeyError as e:
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68 logger.warning('not enrolled {}'.format(r['platewell']))
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69 record = {'platewell': r['platewell'],
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70 'status': pws_map[r['platewell']].status.enum_label(),
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71 'enrollment': ':'.join([study.label,'not_enrolled'])}
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72 writer.writerow(record)
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73 of.close()
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74
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75
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76 if __name__ == "__main__":
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77 main(sys.argv[1:])
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